I was on this media call as well and they basically said that, y'know, functionally the multiplayer is a whole other game. There's some shared assets and stuff, but it's very unique, and that's a lot of it, especially with all the DLC they added over time. So, yeah, they made a call based on how much time and how many resources they said.
Similarly: they thought about changing the animations, updating them, but they discovered that tweaking one iffy animation would often have a cascading effect, breaking ten other things... and just within one game, so then you have to multiply that by three. So they decided to leave animations as-is and focus on other areas of improvement.
ME3 multiplayer being left out does suck a little bit, but also we have to understand as an audience I think that there are limits to what is possible and reasonable with the budget a re-release like this will have, and multiplayer was probably a bridge too far. It is strange in a way as ME3 MP was hugely profitable thanks to the microtransactions and if it saw a revival, EA would probably stand to make money, but maybe they didn't see it being nearly as popular 9 years on.